title: Discovering body site and severity modifiers in clinical texts.
abstract: OBJECTIVE
  To research computational methods for discovering body site and severity modifiers in clinical texts.
  
  
  METHODS
  We cast the task of discovering body site and severity modifiers as a relation extraction problem in the context of a supervised machine learning framework. We utilize rich linguistic features to represent the pairs of relation arguments and delegate the decision about the nature of the relationship between them to a support vector machine model. We evaluate our models using two corpora that annotate body site and severity modifiers. We also compare the model performance to a number of rule-based baselines. We conduct cross-domain portability experiments. In addition, we carry out feature ablation experiments to determine the contribution of various feature groups. Finally, we perform error analysis and report the sources of errors.
  
  
  RESULTS
  The performance of our method for discovering body site modifiers achieves F1 of 0.740-0.908 and our method for discovering severity modifiers achieves F1 of 0.905-0.929.
  
  
  CONCLUSIONS
  Results indicate that both methods perform well on both in-domain and out-domain data, approaching the performance of human annotators. The most salient features are token and named entity features, although syntactic dependency features also contribute to the overall performance. The dominant sources of errors are infrequent patterns in the data and inability of the system to discern deeper semantic structures.
  
  
  CONCLUSIONS
  We investigated computational methods for discovering body site and severity modifiers in clinical texts. Our best system is released open source as part of the clinical Text Analysis and Knowledge Extraction System (cTAKES).
authors.affiliation: Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Dmitriy
authors.initials: D
authors.lastname: Dligach
authors.forename: Steven
authors.initials: S
authors.lastname: Bethard
authors.forename: Lee
authors.initials: L
authors.lastname: Becker
authors.forename: Timothy
authors.initials: T
authors.lastname: Miller
authors.forename: Guergana K
authors.initials: GK
authors.lastname: Savova
mesh_terms: D000715:Anatomy; D057286:Electronic Health Records; D006801:Humans; D009323:Natural Language Processing; D012720:Severity of Illness Index; D060388:Support Vector Machine
keywords: biomedical informatics; information extraction; natural language processing; relation extraction